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The source code for building the mkhssp and hsspconv programs is bundled in the hssp project. The mkhssp executable creates stockholm files with hssp annotations in them. The hsspconv executable converts stockholm to the original hssp format.


The provided Dockerfile sets up a development environment. Build the docker image using the command docker build -t hssp . and run the image in a container, with a local source copy and data files mounted, with the command docker run -v /home/jon/projects/hssp:/app -v /mnt/extra:/srv/data -it hssp.

Download and installation instructions

Source code archives are available here.

Compiling hssp programs



  • Must support at least the c++ 11 standard.

System libraries:

  • libzeep version >= 3.0 (for mkhssp --fetch-dbrefs only)
  • libboost version >= 1.48
  • libz
  • libbz2
  • autoconf
  • automake
  • autotools-dev


Download and uncompress the hssp source code archive (version >= 2.2.6):

tar -zxvf hssp-?.?.?.tar.gz
cd hssp-?.?.?

Configure and build the hssp executables:


To build only one executable of the hssp project, e.g. mkhssp, type:

make mkhssp

To test the mkhssp executable type:


To add the executables to /usr/local/bin type:

sudo make install

Citing hssp

The reference for the new versions of hssp and other protein structure bioinformatics facilities is:

A series of PDB-related databanks for everyday needs
Wouter G. Touw, Coos Baakman, Jon Black, Tim A. H. te Beek,
 E. Krieger, Robbie P. Joosten and Gert Vriend.
Nucl. Acids Res. (2015) 43, D364-D368

The original reference for DSSP is:

Dictionary of protein secondary structure: pattern recognition of
 hydrogen-bonded and geometrical features.
Kabsch W and Sander C, Biopolymers (1983) 22, 2577-2637.

The original reference for HSSP is:

Database of homology-derived protein structures and the structural
 meaning of sequence alignment.
Sander C and Schneider R, Proteins (1991) 9, 56-68.


In 2013, maintenance of hssp has been taken over from Maarten Hekkelman by Coos Baakman. If you want to provide feedback, either send an e-mail to or have a look at existing issues (if necessary, create a new issue).